Contacts of the helix formed by residues 146 - 152 (chain I) in PDB entry 3E1N
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 146 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83I VAL* 5.0 10.3 - - + -
84I GLU* 5.7 4.5 - - + +
141I ILE* 3.8 23.1 + - + +
145I GLY* 1.3 71.3 - - - -
147I GLN* 1.3 59.3 + - + +
149I TYR* 3.2 10.5 + - + +
150I LEU* 2.9 59.7 + - + +
250I SO4 3.2 18.6 + - - +
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Residues in contact with GLN 147 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146I LEU* 1.3 78.1 - - + +
148I ASN* 1.3 65.8 + - - +
150I LEU* 3.3 9.5 + - + +
151I GLN* 3.0 22.6 + - - +
250I SO4 3.2 28.9 + - - +
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Residues in contact with ASN 148 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147E GLN* 3.8 5.1 - - - +
148E ASN* 2.7 42.2 + - - +
151E GLN* 3.4 25.9 + - - +
144I MET* 3.4 33.0 - - + +
145I GLY 3.7 1.2 + - - -
146I LEU 3.4 0.2 - - - -
147I GLN* 1.3 81.0 - - - +
149I TYR* 1.3 64.8 + - - +
151I GLN* 3.4 11.9 + - - -
152I ALA* 3.0 19.8 + - - +
250I SO4 4.4 1.2 + - - -
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Residues in contact with TYR 149 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154E ILE* 5.4 1.3 - - + -
40I LEU* 3.4 27.1 - - + +
83I VAL* 4.1 7.4 - - + -
87I LEU* 3.9 4.9 - - - +
137I GLU* 2.5 45.5 + - - +
140I LEU* 4.3 13.0 - - + -
141I ILE* 3.6 45.3 - - + -
144I MET* 3.7 14.7 - - + +
145I GLY 3.0 19.5 + - - +
146I LEU* 3.4 9.6 - - + +
148I ASN* 1.3 78.4 - - - +
150I LEU* 1.3 74.1 + - + +
152I ALA* 3.1 7.9 + - - +
153I GLN* 3.1 45.4 + - + +
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Residues in contact with LEU 150 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37I LEU* 4.1 24.3 - - + +
83I VAL* 3.8 28.5 - - + -
146I LEU* 2.9 47.9 + - + +
147I GLN* 3.3 7.8 + - - +
149I TYR* 1.3 83.8 - - + +
151I GLN* 1.3 66.0 + - - +
153I GLN* 2.9 20.9 + - + +
154I ILE* 3.8 7.5 + - - +
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Residues in contact with GLN 151 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151E GLN* 3.0 27.1 + - - +
147I GLN 3.0 15.1 + - - +
148I ASN* 3.8 13.6 + - - +
150I LEU* 1.3 75.1 - - - +
152I ALA* 1.3 62.2 + - - +
153I GLN 3.1 1.6 + - - -
154I ILE* 3.4 31.6 + - + +
155I ARG 5.0 0.2 + - - -
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Residues in contact with ALA 152 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151E GLN* 4.0 21.5 - - + +
154E ILE* 4.4 18.6 - - + +
155E ARG* 3.3 27.8 + - - +
39I ARG* 4.6 2.6 + - - +
148I ASN 3.0 14.4 + - - +
149I TYR* 3.3 13.2 - - - +
150I LEU 3.0 0.8 - - - -
151I GLN* 1.3 78.2 - - - +
153I GLN* 1.3 64.7 + - - +
154I ILE 3.5 0.7 - - - -
155I ARG 4.9 0.8 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il